Genetic Variant PPIG:c.929+11A>G (chr2-169631944-A-G) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_004792.3(PPIG):c.929+11A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.566 in 1,569,730 control chromosomes in the GnomAD database, including 254,357 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.60 ( 27735 hom., cov: 32)

Exomes 𝑓: 0.56 ( 226622 hom. )

Consequence

PPIG
NM_004792.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.0310

Variant links:

Genes affected

PPIG (HGNC:14650): (peptidylprolyl isomerase G) Enables cyclosporin A binding activity and peptidyl-prolyl cis-trans isomerase activity. Involved in protein peptidyl-prolyl isomerization. Located in cytosol and nuclear speck. [provided by Alliance of Genome Resources, Apr 2022]

PPIG links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.76).

BP6

Variant 2-169631944-A-G is Benign according to our data. Variant chr2-169631944-A-G is described in ClinVar as [Benign]. Clinvar id is 1266632.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.72 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
PPIG	NM_004792.3 link	c.929+11A>G	intron_variant	Intron 11 of 13	ENST00000260970.8	NP_004783.2	Q13427-1
PPIG	XM_005246966.3 link	c.929+11A>G	intron_variant	Intron 11 of 13		XP_005247023.1	Q13427-1
PPIG	XM_005246967.2 link	c.929+11A>G	intron_variant	Intron 11 of 13		XP_005247024.1	Q13427-1
PPIG	XM_017005302.3 link	c.*170A>G	downstream_gene_variant			XP_016860791.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PPIG	ENST00000260970.8 link	c.929+11A>G		intron_variant	Intron 11 of 13	1	NM_004792.3	ENSP00000260970.3		Q13427-1

Frequencies

GnomAD3 genomes

AF:

0.597

AC:

90664

AN:

151942

Hom.:

27694

Cov.:

show subpopulations

Gnomad AFR

AF:

0.727

Gnomad AMI

AF:

0.498

Gnomad AMR

AF:

0.469

Gnomad ASJ

AF:

0.569

Gnomad EAS

AF:

0.418

Gnomad SAS

AF:

0.631

Gnomad FIN

AF:

0.532

Gnomad MID

AF:

0.570

Gnomad NFE

AF:

0.571

Gnomad OTH

AF:

0.581

GnomAD3 exomes

AF:

0.562

AC:

129529

AN:

230350

Hom.:

36845

AF XY:

0.566

AC XY:

71125

AN XY:

125618

show subpopulations

Gnomad AFR exome

AF:

0.733

Gnomad AMR exome

AF:

0.468

Gnomad ASJ exome

AF:

0.556

Gnomad EAS exome

AF:

0.431

Gnomad SAS exome

AF:

0.628

Gnomad FIN exome

AF:

0.555

Gnomad NFE exome

AF:

0.573

Gnomad OTH exome

AF:

0.549

GnomAD4 exome

AF:

0.563

AC:

797844

AN:

1417670

Hom.:

226622

Cov.:

AF XY:

0.564

AC XY:

398599

AN XY:

706686

show subpopulations

Gnomad4 AFR exome

AF:

0.731

Gnomad4 AMR exome

AF:

0.463

Gnomad4 ASJ exome

AF:

0.555

Gnomad4 EAS exome

AF:

0.412

Gnomad4 SAS exome

AF:

0.619

Gnomad4 FIN exome

AF:

0.558

Gnomad4 NFE exome

AF:

0.563

Gnomad4 OTH exome

AF:

0.563

GnomAD4 genome

AF:

0.597

AC:

90762

AN:

152060

Hom.:

27735

Cov.:

AF XY:

0.590

AC XY:

43886

AN XY:

74332

show subpopulations

Gnomad4 AFR

AF:

0.727

Gnomad4 AMR

AF:

0.469

Gnomad4 ASJ

AF:

0.569

Gnomad4 EAS

AF:

0.418

Gnomad4 SAS

AF:

0.632

Gnomad4 FIN

AF:

0.532

Gnomad4 NFE

AF:

0.571

Gnomad4 OTH

AF:

0.581

Alfa

AF:

0.588

Hom.:

5486

Bravo

AF:

0.595

Asia WGS

AF:

0.580

AC:

2018

AN:

3476

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Sep 14, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

DANN

Benign

0.84

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over